Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

PROVIDER: PRJNA663474 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12642015_1.fastq.gz	Fastqsanger.gz
	SRR12642015_2.fastq.gz	Fastqsanger.gz
	SRR12642016_1.fastq.gz	Fastqsanger.gz
	SRR12642016_2.fastq.gz	Fastqsanger.gz
	SRR12642017_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-02-10 | GSE157951 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

2022-12-15 | GSE190435 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

| PRJNA787124 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

Project description:To explore the function of TTC7B on colon cancer，we established HCT116 TTC7B-KO/OE cell lines. The purpose of this study is to utilize next-generation sequencing techniques to investigate the effects of TTC7B knockout or overexpression on the biological behavior of tumor cells.

2024-10-10 | GSE247502 | GEO

nascent proteome analysis of HCT116 TP53 wild type and TP53 knockout cells treated with Neocarcinostatin (NCS) for 6h

Project description:In order to investigate the potential role of TP53 in regulating translation, HCT116 wild type and TP53 knockout cells were analyzed using both RNA sequencing, Ribosome sequencing and nascent proteome analysis. The cells were treated with 0.2 µg/ml Neocarcinostatin (NCS) to induce DNA damage and activate TP53.

2022-04-27 | PXD029512 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of HCT116 Wild Type and TTC7B-KO/OE Transcriptomes

| PRJNA1039246 | ENA

RNAseq of mutant TP53 HCT116 cell line clones generated via CRISPR editing

Project description:To compare the impact of several TP53 mutant variants in an isogenic setting, different TP53 mutations were introduced in HCT116 colorectal carcinoma cells. This parental cell line is wild-type for TP53 and shows a prototypical p53 response. To ensure unambigous genotype-phenotype correlations, the cell were haploidized prior to CRISPR-editing by introducing inactivating deletions of intronic splicing into one of the two TP53 alleles, leaving only one functional copy of TP53. The remaining TP53 allele was altered by inserting a LoxP-flanked transcriptional stop cassette (Lox-Stop-Lox, LSL) into intron 4, which allowed reversible silencing of TP53 expression. The LSL cassette was then specifically targeted with CRISPR/Cas9 to introduce a variety of different mutant p53 alleles. The competency of the mutated p53 allele to induce a p53 response upon activation using Nutlin-3a was then assessed in an RNAseq experiment.

2024-10-16 | E-MTAB-12734 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Cystine-regulated Transcriptomes

Project description:Purpose: To identify differentially expressed genes regulated by cystine. Methods: HCT116 or RKO cells were cultured for 48 hours in cystine-free or 25μM cystine-containing conditional media, and three independent samples were collected by Trizol reagent and subjected to mRNA-sequencing by the LC Bio (Zhejiang, China) and data analysis Results: we identified cystine upregulated 145 genes and downregulated 169 genes in both HCT116 and RKO cells. GO enrichment analysis revealed that cystine regulated biological functions of G1/S transition of mitotic cell cycle and regulation of DNA replication biosynthetic process.In addition, KEGG enrichment analysis showed that mammalian target of rapamycin (mTOR) signaling pathway, a well-known nutrient sensor, was regulated by cystine. Furthermore,we noticed that SESN2 was one of the most significantly downregulated genes by cystine in both cell lines, and confirmed that cystine activates mTORC1 via the GCN2-ATF4-SESN2 axis in colon cancer cells. Conclusions: Our study established that cystine activates mTORC1 through GCN2-ATF4-SESN2 axis.

2021-04-16 | GSE157894 | GEO

Amplicon-Screening of genomic DNA regions of mutants in the Exon5 R175 position of TP53 in HCT116 cells generated via CRISPR editing

Project description:To compare the impact of CRISPR-egineered R175 TP53 mutant variants in HCT116 and H460 cells, mutations at the amino acid position 175 were generated systematically by CRISP/Cas9 editing. Here, genomic amplicon regions covering the TP53 Exons 5 were sequenced via targeted sequencing.

2024-10-16 | E-MTAB-14322 | biostudies-arrayexpress

Next-generation sequencing facilitates quantitative analysis of miRNAs of cetuximab-resistant colorectal cancer (HCT116-R) cells

Project description:Total RNAs were isolated from three groups, including A group (0×10^9/mL PA-MSHA-treated HCT116 cells), B group (0.3×10^9/mL PA-MSHA-treated HCT116 cells) and C group (0.4×10^9/mL PA-MSHA-treated HCT116 cells). MiRNA sequencing was performed to assess differential expression using next-generation sequencing. The data showed that most miRNAs levels were different in A, B and C groups. Importantly, miR-7-5p was greatly increased in a dose-dependent manner.

2021-08-13 | GSE181843 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data